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Novel metric for hyperbolic phylogenetic tree embeddings
Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8058397/ https://www.ncbi.nlm.nih.gov/pubmed/33928190 http://dx.doi.org/10.1093/biomethods/bpab006 |
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author | Matsumoto, Hirotaka Mimori, Takahiro Fukunaga, Tsukasa |
author_facet | Matsumoto, Hirotaka Mimori, Takahiro Fukunaga, Tsukasa |
author_sort | Matsumoto, Hirotaka |
collection | PubMed |
description | Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. Furthermore, we proposed a novel approach based on our metric to integrate multiple trees for analyzing tree nodes or imputing missing distances. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods. |
format | Online Article Text |
id | pubmed-8058397 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-80583972021-04-28 Novel metric for hyperbolic phylogenetic tree embeddings Matsumoto, Hirotaka Mimori, Takahiro Fukunaga, Tsukasa Biol Methods Protoc Methods Article Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. Furthermore, we proposed a novel approach based on our metric to integrate multiple trees for analyzing tree nodes or imputing missing distances. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods. Oxford University Press 2021-03-27 /pmc/articles/PMC8058397/ /pubmed/33928190 http://dx.doi.org/10.1093/biomethods/bpab006 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Methods Article Matsumoto, Hirotaka Mimori, Takahiro Fukunaga, Tsukasa Novel metric for hyperbolic phylogenetic tree embeddings |
title | Novel metric for hyperbolic phylogenetic tree embeddings |
title_full | Novel metric for hyperbolic phylogenetic tree embeddings |
title_fullStr | Novel metric for hyperbolic phylogenetic tree embeddings |
title_full_unstemmed | Novel metric for hyperbolic phylogenetic tree embeddings |
title_short | Novel metric for hyperbolic phylogenetic tree embeddings |
title_sort | novel metric for hyperbolic phylogenetic tree embeddings |
topic | Methods Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8058397/ https://www.ncbi.nlm.nih.gov/pubmed/33928190 http://dx.doi.org/10.1093/biomethods/bpab006 |
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